Alternatives to taxis in Japan

Navigating central Tokyo by car is an expensive, confusing pain, so the Japanese solution is to take the train out to the general area you want to explore, then rent a car at the station. JR's Ekiren service (aka "Trenta", as in train-rental-car) is the best way to do this, and they often have promotional packages that combine train tickets and rental car.

In addition to "normal" rentals, car sharing/hourly rental is becoming increasingly popular in Japan. Check out Orix, Times Plus and Careco, although there are more hoops to jump through to get set up initially, particularly if you're a visitor instead of a local resident.

Built-in navigation systems in Japanese cars are usually Japanese-only and have an unfamiliar UI if you're used to Garmin & co (pro tip: search by phone number is usually the least bad way to find points of interest). The best workaround is to ignore it completely and use Google Maps (or equivalent) directions on your phone.

Driving in Japan is easier than you imagine it might be, though I would hesitate to drive in Tokyo. The car I rented in Hokkaido in 2016 had navigation in English (I had to specifically request this option when booking), and I needed an International Drivers Permit. The navigation interface was a little unusual relying on phone numbers or points-of-interest that people might want to visit - landmarks, schools, gas stations, etc. Though there didn't seem to be a way to enter a specific address, I found it quite easy to get navigation to some nearby POI, and then zoom in for the last few streets and use it like a regular street map.

The ETC card is for the (very expensive) highway tolls. I had to pay a small extra charge to rent the ETC card, but it gave a discount on the toll rates. In the end, the total discount I obtained was not much more than the rental cost of the ETC card, but it made dealing with the tolls a lot easier and allowed the car rental company to bill me immediately when I returned the car. The toll highways themselves are managed by a regional highway company and the one for Hokkaido had a website that let you calculate the toll for a specific journey - in my case, around $80 for 380km of highway driving! But note that not all stretches of highway are toll roads. The situation could well be a lot different for the highways around Tokyo.

However, perhaps you should compare the car rental prices from Ekiren: $60 or more per day, plus gas; with the price of taxis: around $3 per km. If you are not doing much driving around at your destination and just using it as a means to save a 5km walk, it could turn out to be cheaper taking a taxi when needed.

You can try taking a local bus, but it does take a bit of planning. They are almost always on time, and pretty easy to use. Some of them are pay by trip, and others are pay by distance. You can tell depending if you get on the bus from the front (pay by trip) or the middle (pay by distance). If you get a pay by distance bus you pick up a ticket when you enter the bus, and there is a chart at the front that will have your number and the price if you get off at the current time. The buses have change machines, but getting an IC card would make it much easier.

Hyperdia can be useful to figure out what bus to take. https://www.hyperdia.com/